PMC

The red ticks show the exonic probesets, the gray ticks display the non-exonic probesets (intronic, intergenic and unreliable). In EGFR, KRAS and VEGFA, a total of 51 of 451, 13 of 262 and 25 of 26 exonic probesets were measured respectively. All other probesets were situated outside of exons, i.e. intronic, intergenic or were unreliable.

Row A depicts the association between the tumor shrinkage at week 12 and the exon-level composite score (PCA axis 1) for EGFR, KRAS and VEGFA (left, center and right respectively). The PCA scores are defined as the coordinates of the patients in a new space defined by linear combination of the original probeset intensity values using principal component analysis. The patients with EGFR mutations are marked in red, those with non-available mutational status are shown as empty circles. The row B shows the significance of the correlation (−log(-value)) between each exon probeset and the tumor shrinkage at week 12. The position of the exons is shown in blue.

The left panel depicts the correlation between the expression intensity of the exon 18-EGFR (probeset 3002770) and the tumor shrinkage at week 12. The vertical line shows the median expression intensity of EGFR probeset 3002770. Patients with EGFR mutations are shown as red plain dots and labelled accrodingly. Patients with non-available mutational status are displayed as empty circles. The central panel represents the receiver operating characteristic (ROC) curve showing the sensitivity/specificity of a test based on the expression level of EGFR probeset 3002770 to classify responders (tumor shrinkage at week 120/20/30%) vs. non-responders (tumor shrinkage at week 120/20/30%). The plain dots depict the true positive and false positive rates obtained by fixing the cutoff value to the median expression level of EGFR 3002770. The waterfall plot (right panel) displays the change in tumor size at week 12 ordered from left to right. The colors are defined by the expression intensity of EGFR 3002770 dichotomized by the median of the expression evel (blue: low expression intensities; red: high expression intensities).